Fullmetal Alchemist. Shrinking can take place at anytime in the storyline, during the war with the Homunculi, after the war. As long as you lay out your ideas beforehand I won't hold anything against you.
1. Edward shrinks mysteriously in his hospital bed after the incident at the fifth Laboratory, shortly after 2nd lieutenant Maria Ross walks into the room to check up on him. Surprised to see that he’s missing.
2. Before meeting up with Riza Hawkeye for a secret rondevu to exchange information about the homunculus Roy Mustang shrinks, only to be found by the giant blonde.